Scofield tells the team about the extra member and they decide to cast out Bagwell; but he informs them that his cousin knows the plan outside and he'll call the authorities if Bagwell is not included. Abruzzi's men find Bagwell's cousin; but the man and his little child is killed in the struggle. Abruzzi feels guilty for everything he's done; but he decides to take care of Bagwell anyway. Bagwell swears to atone for his mistakes like Abruzzi did. The latter spares the former, giving him a chance to slit the latter's throat. Meanwhile, Lincoln is forced to assault Geary to cover for the team, which results in his abduction by the guards. Delgado informs Sucre that she is pregnant and he realizes that he tells her that he is getting out soon. Bellick forces Apolskis to spy on Scofield to avoid solitary for stealing from Geary. In the meantime, Savrinn is taken to a hospital. Hale feels guilty for his actions and plans to escape with his family. He calls Donovan and makes an arrangement.

Donovan meets Hale, who reveals that Steadman is alive. Before he can give her anything, Kellerman arrives and kills Hale; she escapes after watching the murder. Meanwhile, Abruzzi is taken by a helicopter outside the prison for better care and the odd man problem is solved. Lincoln is beaten by the guards and thrown in the solitary. Pope denies Scofield's request to meet Lincoln. Scofield decides to suspend the plan, but the others push to leave without Lincoln now that everything is ready. Franklin calls his brother-in-law, the only one in the family who knows he is in prison, and tells him to arrange for the plan. Scofield manages to send Lincoln a drug with a message when to take it. The team deliberately makes a mess in the room and Bellick forces them to stay and work until night, giving them the chance to escape. When the time comes, Lincoln takes the drug, gets sick and is taken to the infirmary; and the team proceeds to the room under there; but they realize that the tube Scofield made a hole in is changed with a reinforced one, ruining the breakout.

Before Bagwell can make any move, the team hears a guard coming. They hide and after he leaves, they return to their cells without arousing suspicion. Donovan and Savrinn arrange for an appellate court to reveal what she saw. Scofield learns from Westmoreland that the execution will be delayed for weeks if the electric chair has a malfunctioning, a conversation that is heard by Apolskis. Scofield uses a mouse to cut the power of the chair. In the court, Donovan has no evidence for what she saw; and the government attorney presents documents that state no agents with names Kellerman or Hale have ever worked in Secret Service. Bellick forces Apolskis to share what he knows and he tells him what he heard and the latter solves the problem before the execution time comes, surprising Scofield. Lincoln has already surrendered to his apparent fate. He talks to L.J. on the phone and says goodbye to Scofield and Donovan, who has failed at the appeal. Lincoln enters the execution room.

Three years ago, Scofield was living a comfortable life while Lincoln was saddled with debts. His debts were paid by a man who forced him to kill Steadman in exchange. After Lincoln's arrest, Scofield blamed him for not using his share of the life insurance properly and ruining his life. Donovan revealed to Scofield that there had been no life insurance when his mother had died; Lincoln borrowed the money for Scofield to thrive and kept the truth hidden. Feeling responsible, Scofield planned the breakout. Tancredi used rehabilitation to quit addiction, where Bellick offered her the job in Fox River. Sucre attempted to rob a store to buy Delgado a suiting ring; Hector called the police and Sucre was arrested. Franklin served in the army when he saw prisoner torture. He reported the crime; but he was fired to prevent the scandal. He had to earn money by illegal goods transferring and was arrested, but kept it hidden from his family. Bagwell was in love with a widow who had two children. She had him arrested when she realized that he was wanted for child rape and murder. He promised to find her when he got out.

Tancredi reports what she found to Pope, who sends Scofield to solitary after he refuses to talk. Scofield apparently gets mentally ill. Bellick decides to bring more professional workers for the room. The team realizes that the hole must be covered soon. Since Sucre's cell has the only way to the room, he is picked for the job. He covers the hole and starts running in the courtyard before getting caught. With material provided by Bagwell, Sucre relatively justifies his action, but goes to the solitary anyway. Apolskis tells Bellick that the team is planning something related to the floor; but the latter doesn't find the hole because it was covered by Sucre in time. Because of the disappointment, Bellick puts Apolskis in a violent inmate named Avocado's cell. Scofield is taken to the asylum, where he is revealed to be healthy and this was a plan to reach Patoshik, who can help the former with his tattoo; but the latter doesn't remember anything. Meanwhile, Donovan's group recovers Quinn's cell phone to find clues. In the well, L.J. sees the name 'Kellerman' carved by Quinn. He finds Kellerman's house and ambushes him alone. The police arrive and arrest L.J.